VEMDP 2018

Verification of Engineered Molecular Devices and Programs

July 19, 2018, Oxford, United Kingdom
An affiliated workshop of CAV 2018
Abstract SubmissionApril 15, 2018 April 23, 2018
NotificationMay 15, 2018
Camera-readyMay 25, 2018
WorkshopJuly 19, 2018

The VEMDP workshop will take place Thursday July 19, 2018.
The workshop dinner will take place Wednesday July 18, 2018, in Magdalen College, 7pm.

The workshop program can also be found on the FLoC website: VEMDP program on the FLoC webpage

Workshop schedule

09:00 - 10:00 Controlling Assembly and Function of DNA Nanostructures and Molecular Machinery
Andrew J. Turberfield (Invited Talk)
10:00 - 10:20 Computing Properties of Stable Configurations of Thermodynamic Binding Networks
Keenan Breik, Chris Thachuk, Marijn Heule and David Soloveichik
Session break
11:00 - 11:20 Rule-Based Gillespie Simulation of Chemical Systems
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle and Peter F. Stadler
11:20 - 11:40 Rule-based Design of Computational DNA Devices
Carlo Spaccasassi, Matthew Lakin and Andrew Phillips
11:40 - 12:00 Noise Control for Molecular Computing
Tomislav Plesa, Radek Erban, Konstantinos Zygalakis and David Anderson
12:00 - 12:20 Molecular Filters for Noise Reduction
Luca Laurenti, Marta Kwiatkowska, Attila Csikász-Nagy and Luca Cardelli
Session break
14:00 - 15:00 Uncovering the Biological Programs that Govern Development
Sara-Jane Dunn (Invited Talk)
15:00 - 15:10 Poster: Bayesian Verification of Chemical Reaction Networks
Gareth Molyneux, Viraj Brian Wijesuriya and Alessandro Abate
15:10 - 15:20 Poster: Computational Approaches for the Programmed Assembly of Nanocellulose Meshes
Alexandru Amarioarei, Frankie Spencer, Trandafir Romica, Gefry Barad, Ana Maria Dobre, Corina Itcus, Iris Tusa, Mihaela Paun, Andrei Paun and Eugen Czeizler
Session break
16:00 - 16:20 Equivalence of Chemical Reaction Networks in a CRN-to-DNA Compiler Framework
Stefan Badelt and Erik Winfree
16:20 - 16:40 Using Transitivity and Modularity in Chemical Reaction Network Bisimulation
Robert F. Johnson
16:40 - 17:00 Conservative Approximations of Polymers
Ken Chanseau Saint-Germain and Jerome Feret
17:00 - 17:20 Executable Biochemical Space for Specification and Analysis of Biochemical Systems
Matej Troják, Jakub Šalagovič, David Šafránek, Jan Červený, Lubos Brim and Matej Hajnal
17:20 - 17:40 Formal Verification of Network-Based Biocomputation Circuits
Hillel Kugler, Till Korten, Stefan Diez and Dan Nicolau Jr.